BUGSI Benchmarking Report
Date: 08 January 2025
Summary
Data Matrix
Reference Match (RM): Isoform is FSM and within 50 bp of annotated transcription start and end sites.
Full Splice Match (FSM): Isoform with identical exon count and matching internal junctions; start and end may vary.
Incomplete Splice Match (ISM): Isoform missing some 5’ exons but with matching internal junctions.
Novel In Catalog (NIC): Isoform uses known splice sites but lacks FSM or ISM match.
Novel Not in Catalog (NNC): Isoform contains unannotated splice sites.
Genic Intron: Isoform entirely within an annotated intron.
Evaluation Metrics
1. Sensitivity (Sn):
\[ \text{Sn} = \frac{\text{Unique (TP)}}{\text{Total BUGSI Genes}} \]
2. Non-redundant Precision (nrPre):
\[ \text{nrPre} = \frac{\text{TP}}{\text{Total BUGSI Match Transcripts}} \]
3. Precision (Pre):
\[ \text{Pre} = \frac{\text{TP} + \text{PTP}}{\text{Total BUGSI Match Transcripts}} \]
4. Positive Detection Rate (PDR):
\[ \text{PDR} = \frac{\text{Unique (TP + PTP)}}{\text{Total BUGSI Genes}} \]
5. False Discovery Rate (FDR):
\[ \text{FDR} = \frac{\text{Total BUGSI Match Transcripts} - \text{TP}}{\text{Total BUGSI Match Transcripts}} \]
6. False Detection Rate:
\[ \text{False Detection Rate} = \frac{\text{FP}}{\text{Total BUGSI Match Transcripts}} \]
7. Redundancy (1/Red):
\[ \text{Redundancy (1/Red)} = \frac{\text{TP + PTP}}{\text{Unique (TP + PTP)}} \]